Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate Echvi_2204 Echvi_2204 ABC-type antimicrobial peptide transport system, ATPase component
Query= reanno::pseudo3_N2E3:AO353_03040 (254 letters) >FitnessBrowser__Cola:Echvi_2204 Length = 240 Score = 137 bits (346), Expect = 2e-37 Identities = 87/244 (35%), Positives = 138/244 (56%), Gaps = 18/244 (7%) Query: 4 LEVQDLHKRY--GSHEV--LKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGK 59 +E +++ K Y G+ +V LK V++ G+ ++ +G SGSGKST + I L+ P AG Sbjct: 5 IETKEIKKTYVMGAEKVQALKSVTIDIIKGEYVAFMGPSGSGKSTLMNIIGCLDTPTAGN 64 Query: 60 ILLNNEELKLVANKDGALKAADPKQLQRMRSR-LSMVFQHFNLWSHMTAMENIMEAPVHV 118 +LNN+++ + + L +R++ + VFQ FNL T +EN+ P+ Sbjct: 65 YILNNKDVSHMTENE----------LAEIRNKEIGFVFQTFNLLPRATCLENVA-LPLIY 113 Query: 119 LGMSKAEAREKAELYLAKVGVSHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTS 178 G SK++ +KA L L VG+ R P +SGG++QRVAIARAL +P ++L DEPT Sbjct: 114 AGYSKSDREDKAFLALKSVGLEDRIHHKPNELSGGQRQRVAIARALVNDPSIILADEPTG 173 Query: 179 ALDPELVGDVLKVMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVE-ESGNPREVL 237 LD + D++ + L Q+G T+++VTHE A ++++V L G+VE + NP Sbjct: 174 NLDTKTSYDIMNLFDELHQKGNTIIMVTHEDDIA-HYAHRIVRLRDGLVETDQNNPNPTR 232 Query: 238 VNPQ 241 N Q Sbjct: 233 NNFQ 236 Lambda K H 0.317 0.131 0.364 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 138 Number of extensions: 6 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 254 Length of database: 240 Length adjustment: 24 Effective length of query: 230 Effective length of database: 216 Effective search space: 49680 Effective search space used: 49680 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory